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Suggestions on PR: Calculate per callset stats on gnomAD v4.1 per sample variant counts #614

Merged
merged 32 commits into from
May 24, 2024
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Merged

Suggestions on PR: Calculate per callset stats on gnomAD v4.1 per sample variant counts #614

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98e7cd1
Move some of the filter expression functionality to gnomad_methods
jkgoodrich May 9, 2024
61e8638
Changes needed while testing
jkgoodrich May 9, 2024
10b16bb
Convert filtering group to array to avoid class too large error
jkgoodrich May 9, 2024
4a74c99
Clean-up main a bit
jkgoodrich May 9, 2024
f2180eb
Clean-up main a bit
jkgoodrich May 9, 2024
369b1f5
- Add some clear metadata for the filter groups for easier parsing.
jkgoodrich May 10, 2024
42675ff
Annotate globals onto the output HT
jkgoodrich May 10, 2024
4d9312d
Add extra common filter group
jkgoodrich May 10, 2024
2c3944e
Add extra common filter group
jkgoodrich May 13, 2024
d44d6d0
Add more detained doc string to `get_summary_stats_filter_groups_ht`
jkgoodrich May 20, 2024
8b529b8
Apply suggestions from code review
jkgoodrich May 20, 2024
1e7b5f7
Only define `COMMON_FILTER_COMBOS` once
jkgoodrich May 20, 2024
4c0d684
Don't include keys in the naming if they have `csq` in the name
jkgoodrich May 20, 2024
374c3fb
Add clear comments and documentation to `get_filter_group_meta`
jkgoodrich May 20, 2024
4ccf6a9
Make various changes to names of filter groups and filter group meta
jkgoodrich May 22, 2024
61b010d
remove unused imports
jkgoodrich May 22, 2024
043d5e1
Update comments and doctrings, primarily for get_filter_group_meta
jkgoodrich May 22, 2024
295a6c3
Update docstring in get_summary_stats_filter_groups_ht
jkgoodrich May 22, 2024
47787f5
Update compute_agg_sample_stats to work with the new input format
jkgoodrich May 22, 2024
7a618f2
loftee_labels -> loftee_label and add logger warn if a filter group i…
jkgoodrich May 22, 2024
b2ac083
Fix example in get_filter_group_meta
jkgoodrich May 23, 2024
a365857
Update globals to create missing loftee combinations
jkgoodrich May 23, 2024
3def23a
Move loftee flags to only LOF_FILTERS_FOR_COMBO
jkgoodrich May 23, 2024
629dc93
Move loftee label to only LOF_FILTERS_FOR_COMBO
jkgoodrich May 23, 2024
a33e653
loftee_HC -> loftee_label
jkgoodrich May 23, 2024
4fb0fd6
Add more options to the get_filter_group_meta docstring
jkgoodrich May 23, 2024
c7be055
Make parameters optional in get_filter_group_meta so it's more genera…
jkgoodrich May 23, 2024
a595372
Update comment
jkgoodrich May 24, 2024
643c03a
Apply suggestions from code review
jkgoodrich May 24, 2024
1ab0200
Rename arguments in get_filter_group_meta
jkgoodrich May 24, 2024
6f9c331
Merge branch 'jg/move_some_stats_functionality_to_methods' of https:/…
jkgoodrich May 24, 2024
8acafb4
Move generate_filter_combinations and get_filter_group_meta to gnomad…
jkgoodrich May 24, 2024
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